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protocols::protein_interface_design::filters::RmsdSimpleFilter Class Reference

#include <RmsdSimpleFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::RmsdSimpleFilter:
Inheritance graph
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Public Member Functions

 RmsdSimpleFilter ()
 
 RmsdSimpleFilter (core::Real const threshold, core::pose::PoseOP reference_pose)
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
core::Real compute (core::pose::Pose const &pose) const
 
 ~RmsdSimpleFilter () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

void superposition_transform (core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &ref_coords, ObjexxFCL::FArray2_double &coords, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB) const
 Superposition_transform wrapper (as in Alex Ford code protocols/toolbox/superimpose.[cc,hh]) More...
 
core::Real rmsd_bb (core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB) const
 Function that performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Uses a reference to the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses. More...
 
core::Real dist_bb (core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB) const
 Returns the BB distance of two poses respect to indexes. More...
 

Private Attributes

core::Real threshold_
 
core::pose::PoseCOP reference_pose_
 
core::Size target_chain_
 
core::Size do_align_
 
bool b_target_chain_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::RmsdSimpleFilter::RmsdSimpleFilter ( )
protocols::protein_interface_design::filters::RmsdSimpleFilter::RmsdSimpleFilter ( core::Real const  threshold,
core::pose::PoseOP  reference_pose 
)

References reference_pose_, and threshold_.

protocols::protein_interface_design::filters::RmsdSimpleFilter::~RmsdSimpleFilter ( )
overridedefault

Member Function Documentation

bool protocols::protein_interface_design::filters::RmsdSimpleFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), threshold_, and protocols::protein_interface_design::filters::TR().

std::string protocols::protein_interface_design::filters::RmsdSimpleFilter::class_name ( )
static
protocols::filters::FilterOP protocols::protein_interface_design::filters::RmsdSimpleFilter::clone ( ) const
overridevirtual
core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::compute ( core::pose::Pose const &  pose) const
core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::dist_bb ( core::pose::Pose const &  poseA,
utility::vector1< core::Size > const &  positions_to_alignA,
core::pose::Pose const &  poseB,
utility::vector1< core::Size > const &  positions_to_alignB 
) const
private

Returns the BB distance of two poses respect to indexes.

References core::pose::Pose::residue(), protocols::cluster::calibur::RMSD(), and core::conformation::Residue::xyz().

Referenced by compute().

protocols::filters::FilterOP protocols::protein_interface_design::filters::RmsdSimpleFilter::fresh_instance ( ) const
overridevirtual
std::string protocols::protein_interface_design::filters::RmsdSimpleFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::protein_interface_design::filters::RmsdSimpleFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References b_target_chain_, do_align_, reference_pose_, core::pose::saved_native_pose(), core::pose::saved_reference_pose(), target_chain_, threshold_, and protocols::protein_interface_design::filters::TR().

void protocols::protein_interface_design::filters::RmsdSimpleFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::protein_interface_design::filters::RmsdSimpleFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::rmsd_bb ( core::pose::Pose const &  poseA,
utility::vector1< core::Size > const &  positions_to_alignA,
core::pose::Pose const &  poseB,
utility::vector1< core::Size > const &  positions_to_alignB 
) const
private

Function that performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Uses a reference to the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses.

References core::pose::Pose::residue(), protocols::cluster::calibur::RMSD(), superposition_transform(), and core::conformation::Residue::xyz().

Referenced by compute().

void protocols::protein_interface_design::filters::RmsdSimpleFilter::superposition_transform ( core::Size  natoms,
ObjexxFCL::FArray1_double const &  weights,
ObjexxFCL::FArray2_double &  ref_coords,
ObjexxFCL::FArray2_double &  coords,
numeric::xyzMatrix< core::Real > &  RotM,
numeric::xyzVector< core::Real > &  TvecA,
numeric::xyzVector< core::Real > &  TvecB 
) const
private

Superposition_transform wrapper (as in Alex Ford code protocols/toolbox/superimpose.[cc,hh])

References protocols::toolbox::fit_centered_coords(), and protocols::toolbox::reset_x().

Referenced by rmsd_bb().

Member Data Documentation

bool protocols::protein_interface_design::filters::RmsdSimpleFilter::b_target_chain_
private

Referenced by compute(), and parse_my_tag().

core::Size protocols::protein_interface_design::filters::RmsdSimpleFilter::do_align_
private

Referenced by compute(), and parse_my_tag().

core::pose::PoseCOP protocols::protein_interface_design::filters::RmsdSimpleFilter::reference_pose_
private
core::Size protocols::protein_interface_design::filters::RmsdSimpleFilter::target_chain_
private

Referenced by compute(), and parse_my_tag().

core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::threshold_
private

The documentation for this class was generated from the following files: